The encapsulation of subnanometric metal entities (isolated metal atoms and metal clusters with a few atoms) in porous materials such as zeolites can be an effective strategy for the stabilization of those metal species and therefore can be further used for a variety of catalytic reactions. However, owing to the complexity of zeolite structures and their low stability under the electron beam, it is challenging to obtain atomic-level structural information of the subnanometric metal species encapsulated in zeolite crystallites. In this protocol, we show the application of a scanning transmission electron microscopy (STEM) technique that records simultaneously the high-angle annular dark-field (HAADF) images and integrated differential phase-contrast (iDPC) images for structural characterization of subnanometric Pt and Sn species within MFI zeolite. The approach relies on the use of a computational model to simulate results obtained under different conditions where the metals are present in different positions within the zeolite. This imaging technique allows to obtain simultaneously the spatial information of heavy elements (Pt and Sn in this work) and the zeolite framework structure, enabling direct determination of the location of the subnanometric metal species. Moreover, we also present the combination of other spectroscopy techniques as complementary tools for the STEM-iDPC imaging technique to obtain global understanding and insights on the spatial distributions of subnanometric metal species in zeolite structure. These structural insights can provide guidelines for the rational design of uniform metal-zeolite materials for catalytic applications.